AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i347_weak8_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yprA	102	similar to ATP-dependent helicase
#2	ypqE	137	similar to phosphotransferase system enzyme II

Motif number 1

TTTATACAGTTGAATAAAAAAAGCAAGGCATAC	1	18	0	TGAATAAAAG	    0.993031	-85
TTTATTCAACTGTATAAAATTTGCACCTAGCCA	1	33	1	TGTATAAATG	    0.949597	-70
ACGCATAATCTGGTTAAAAAAGGCGGTGGCGAT	2	12	0	TGGTTAAAAG	    0.980912	-126
TGTTATAAATTGAAGCAAAATTGAAAGTGTGGT	2	58	1	TGAAGAAAAG	    0.994222	-80
ATTGAAAGTGTGGTTAAATAGTGGTGAATGAAG	2	77	1	TGGTTAATAG	    0.957187	-61
TAGTGGTGAATGAAGGGATAACGGTTGAAGTGA	2	95	1	TGAAGGATAG	    0.980535	-43
GGATAACGGTTGAAGTGAATGAGAAGGGAGAAA	2	110	1	TGAAGGAATG	    0.980534	-28
          ***** ****  *

Masking position 8
Map Score:   7.67995

Number of sites scoring better than the average of aligned sites = 725
Number in coding regions = 624
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 2

GCAAATTTTATACAGTTGAATAAAAAAAGC	1	27	0	TACAGTTGAA	     0.96385	-76
CTTTGTCAAGTACAGTTTACCGAATATTTG	1	72	0	TACAGTTTAC	    0.832897	-31
GTACTTGACAAAGAGGTGTAAAGA      	1	89	1	AAGAGGTGTA	    0.916175	-14
TAGACGCATAATCTGGTTAAAAAAGGCGGT	2	18	0	ATCTGGTTAA	    0.935778	-120
AAAATTGAAAGTGTGGTTAAATAGTGGTGA	2	74	1	GTGTGGTTAA	    0.866799	-64
TGTGGTTAAATAGTGGTGAATGAAGGGATA	2	85	1	TAGTGGTGAA	    0.981353	-53
ATGAAGGGATAACGGTTGAAGTGAATGAGA	2	104	1	AACGGTTGAA	    0.951554	-34
          **********

Masking position 7
Map Score:   2.33887

Number of sites scoring better than the average of aligned sites = 1269
Number in coding regions = 1061
Number in noncoding regions = 208
Number of orfs with sites within 600 bp upstream = 190
Fraction of orfs with sites within 600 bp upstream = 0.0305172


Motif number 3

          **********

No masking
Map Score:   -1.75204e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

          **********

No masking
Map Score:   -1.75204e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -1.75204e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0